`
t <- importC(con="mynorm_500000_iced.matrix", xgi="../../raw/500000/dixon_2M_500000_abs.bed") # worked but after using running "ice" script from HiC-Pro package, which finally gave the normalized 3-column output.
include your problematic code here with any corresponding output
head(summary(t))
Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'head': error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': error in evaluating the argument 'x' in selecting a method for function 't': no method or default for coercing “ddiMatrix” to “dgTMatrix”
please also include the results of running the following in an R session
sessionInfo( )
R version 4.1.2 (2021-11-01) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19043)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
system code page: 65001
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods
[9] base
other attached packages:
[1] HiTC_1.38.0 bigmemory_4.6.1 data.table_1.14.2 rtracklayer_1.54.0
[5] GenomicRanges_1.46.1 GenomeInfoDb_1.30.1 IRanges_2.28.0 S4Vectors_0.32.3
[9] BiocGenerics_0.40.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.8.3 bigmemory.sri_0.1.3 rstudioapi_0.13
[4] XVector_0.34.0 zlibbioc_1.40.0 GenomicAlignments_1.30.0
[7] uuid_1.1-0 BiocParallel_1.28.3 lattice_0.20-45
[10] rjson_0.2.21 tools_4.1.2 grid_4.1.2
[13] SummarizedExperiment_1.24.0 Biobase_2.54.0 matrixStats_0.61.0
[16] yaml_2.2.2 crayon_1.5.1 BiocIO_1.4.0
[19] Matrix_1.4-0 GenomeInfoDbData_1.2.7 RColorBrewer_1.1-3
[22] restfulr_0.0.13 bitops_1.0-7 RCurl_1.98-1.6
[25] DelayedArray_0.20.0 compiler_4.1.2 MatrixGenerics_1.6.0
[28] Biostrings_2.62.0 Rsamtools_2.10.0 XML_3.99-0.8
```
Hello Which type of data do you try to import ? Please add the command line you used. Best
Hi Nicolas,
Many thanks for your quick response!
I am trying to load results obtained from HiCpro run using test data provided with the package. Below given the command hic <- importC("../../raw/500000/dixon_2M_500000.matrix",xgi.bed = "../../raw/500000/dixon_2M_500000_abs.bed")
I have tried to run importC function statements step-wise and I observed the following:
read.table() function within importC() was not able to load iced.matrix, then I manually checked the iced.matrix and figured out the file is not 3-column as required by the function
The normalized contact map (ice command) is producing multiple column file using rather correct 3-column raw contact map input. I tried to fix it by running "ice" script from HiC-Pro package, which finally gave the normalized 3-column output. Further, using this file, importC() seems to work fine but when I launched head(summary(hic)) it is throwing the error below:
Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'head': error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': error in evaluating the argument 'x' in selecting a method for function 't': no method or default for coercing “ddiMatrix” to “dgTMatrix”
Now, I have no idea how to solve this error.
Thank you, Best, Shikha
Any solutions!